Dependency analysis on package clipper

General information

Bioconductor link link
Package version1.36.0
Number of strong dependencies112
Number of all dependencies143
Number of parent packages11
Max heaviness from parent packages84
Total heaviness from parent packages90
Number of parent packages (including Suggests and Enhances)19
Max co-heaviness from parent packages ("qpgraph" and "KEGGgraph")3

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of clipper and columns are the dependency packages that each parent package brings in. On the right side of the heatmap, there are three barplot annotations: 1. number of imported functions/S4 methods/S4 classes from parent packages; 2. number of dependency packages from each parent package; 3. heaviness of each parent package on clipper.

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests Enhances methods utils stats graphics grDevices stats4 grid tools parallel BiocGenerics graph pkgconfig RCurl bitops jsonlite R6 rlang glue fastmap lattice magrittr Rcpp Biobase httr curl mime openssl crayon askpass vctrs sys cli BH Matrix Rgraphviz XML S4Vectors AnnotationDbi IRanges GenomeInfoDb DBI RSQLite KEGGREST GenomeInfoDbData XVector Biostrings bit64 blob memoise plogr png zlibbioc digest rappdirs bit cachem BiocManager stringr yaml stringi ellipsis lifecycle pillar fansi utf8 RBGL igraph RcppEigen RcppArmadillo annotate BiocParallel GenomicRanges GenomicFeatures mvtnorm qtl xtable futile.logger snow codetools BiocIO rtracklayer biomaRt lambda.r futile.options Rsamtools GenomicAlignments restfulr progress BiocFileCache xml2 formatR Rhtslib SummarizedExperiment rjson hms prettyunits dbplyr dplyr filelock MatrixGenerics DelayedArray assertthat purrr tibble tidyselect withr generics matrixStats htmltools evaluate base64enc fs bookdown knitr rmarkdown jquerylib xfun tinytex highr bslib sass org.Hs.eg.db RJSONIO uuid uchardet base64url IRkernel IRdisplay RColorBrewer backports repr pbdZMQ 0 2 4 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents graph Matrix methods corpcor Rcpp Biobase RBGL igraph KEGGgraph gRbase qpgraph RUnit BiocGenerics MASS ALL BiocStyle hgu95av2.db graphite RCy3 In total 112 packages are required directly or indirectly (143) when installing 'clipper' (1.36.0) Depends Imports Suggests Enhances Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'clipper' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

"Import" information is from the NAMESPACE file of clipper.

imports: number of imported functions/objects; importMethods: number of imported S4 methods; importClasses: number of imported S4 classes.

Required packages: number of strong dependency packages for each of the parent package (or in other words, number of dependency packages the parent package brings in).

Heaviness from parent on clipper: number of required packages that can be reduced if moving parent package to Suggests of clipper.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on clipper
graph Depends The whole set of functions/methods/classes from parent package is imported to the namespace of clipper. 6 0
Matrix Depends The whole set of functions/methods/classes from parent package is imported to the namespace of clipper. 7 0
qpgraph Imports 1 0 0 103 84
gRbase Imports The whole set of functions/methods/classes from parent package is imported to the namespace of clipper. 21 4
corpcor Imports 1 0 0 1 1
KEGGgraph Imports The whole set of functions/methods/classes from parent package is imported to the namespace of clipper. 13 1
methods Imports 1 0 0 0 0
Rcpp Imports The whole set of functions/methods/classes from parent package is imported to the namespace of clipper. 2 0
Biobase Imports 0 1 1 5 0
RBGL Imports 1 0 0 8 0
igraph Imports 5 0 0 10 0
BiocStyle Suggests No object is imported into the namespace of clipper. 30 14
hgu95av2.db Suggests No object is imported into the namespace of clipper. 46 2
RUnit Suggests No object is imported into the namespace of clipper. 3 1
MASS Suggests No object is imported into the namespace of clipper. 5 1
ALL Suggests No object is imported into the namespace of clipper. 6 1
graphite Suggests No object is imported into the namespace of clipper. 47 1
BiocGenerics Suggests No object is imported into the namespace of clipper. 4 0
RCy3 Enhances No object is imported into the namespace of clipper. 46 15

Analysis was done with pkgndep.